Aquarium Python Scripting Demo

This is a demo for Python scripting to accessing Aquarium using Trident.

This demo uses pydent 0.0.35. Version 0.1.5a6 is also available.

Note: The use of Docker is technically not necessary, but it is used here to manage the Python environment.

Getting started

The example scripts assume a file resources.py that defines the values login, password and url. This file can be constructed by first running the command

cp resources.py-temp resources.py

and then changing the values to match your Aquarium account.

The import

from resources import resources

should be included at the top of each script.

The command

session = AqSession(
        resources['aquarium']['login'],
        resources['aquarium']['password'],
        resources['aquarium']['aquarium_url']
    )

creates the session object to make queries to Aquarium.

Note that resources.py contains secrets that should not be checked into your version control.

Samples

To get a sample, the best strategy is to query by the sample name. For instance, using the BIOFAB production system, the query

sample = session.Sample.find_by_name('IAA1-Nat-F')

returns the sample with the name IAA1-Nat-F. We can inspect the type of the sample with

print(sample.sample_type.name)

which shows this sample is a primer. Running

print(sample.properties)

will show the properties that define this sample as a case of the sample type (a primer should have an overhang and anneal sequence, and an annealing temperature).

Each sample has a name, project, description, properties and sample_type properties.

To create a sample linked to the database, use the Sample.new function:

primer_type = session.SampleType.find_by_name('Primer')
sample = session.Sample.new(
    name="Example Primer",
    project="trident-demo",
    description="primer created with trident",
    sample_type_id=primer_type.id,
    properties={
        'Overhang Sequence': 'AAAAA',
        'Anneal Sequence': 'GGGGGGGG',
        'T Anneal': 70
    }
)

To save this sample object to Aquarium, it is necessary to run the command

sample.save()

(Don't do save this demo object to a production system!)

Plans

Using Trident makes it possible to create complex plans that are tedious to create with the graphical planner in Aquarium.

This section shows creating plans in pydent 0.0.35 The next release includes simplified planning.

Provenance

For getting information about previous runs, we are going to demo the aquarium-provenance package based on Trident.